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Aliases for WHSC1 Gene

Aliases for WHSC1 Gene

  • Wolf-Hirschhorn Syndrome Candidate 1 2 3
  • Nuclear SET Domain-Containing Protein 2 3 4
  • EC 2.1.1.43 4 64
  • MMSET 3 4
  • NSD2 3 4
  • TRX5 3 4
  • Multiple Myeloma SET Domain Containing Protein Type III 3
  • Probable Histone-Lysine N-Methyltransferase NSD2 3
  • Multiple Myeloma SET Domain-Containing Protein 4
  • Wolf-Hirschhorn Syndrome Candidate 1 Protein 4
  • IL5 Promoter REII Region-Binding Protein 3
  • Histone-Lysine N-Methyltransferase NSD2 3
  • Trithorax/Ash1-Related Protein 5 3
  • Protein Trithorax-5 4
  • KIAA1090 4
  • REIIBP 3
  • WHS 3

External Ids for WHSC1 Gene

Summaries for WHSC1 Gene

Entrez Gene Summary for WHSC1 Gene

  • This gene encodes a protein that contains four domains present in other developmental proteins: a PWWP domain, an HMG box, a SET domain, and a PHD-type zinc finger. It is expressed ubiquitously in early development. Wolf-Hirschhorn syndrome (WHS) is a malformation syndrome associated with a hemizygous deletion of the distal short arm of chromosome 4. This gene maps to the 165 kb WHS critical region and has also been involved in the chromosomal translocation t(4;14)(p16.3;q32.3) in multiple myelomas. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. Some transcript variants are nonsense-mediated mRNA (NMD) decay candidates, hence not represented as reference sequences. [provided by RefSeq, Jul 2008]

GeneCards Summary for WHSC1 Gene

WHSC1 (Wolf-Hirschhorn Syndrome Candidate 1) is a Protein Coding gene. Diseases associated with WHSC1 include wolf-hirschhorn syndrome and myeloma. Among its related pathways are Transcriptional misregulation in cancer and Lysine degradation. GO annotations related to this gene include chromatin binding and histone-lysine N-methyltransferase activity. An important paralog of this gene is EHMT1.

UniProtKB/Swiss-Prot for WHSC1 Gene

  • Histone methyltransferase with histone H3 Lys-27 (H3K27me) methyltransferase activity. Isoform RE-IIBP may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.

Gene Wiki entry for WHSC1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WHSC1 Gene

Genomics for WHSC1 Gene

Genomic Location for WHSC1 Gene

Start:
1,871,396 bp from pter
End:
1,982,207 bp from pter
Size:
110,812 bases
Orientation:
Plus strand

Genomic View for WHSC1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for WHSC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WHSC1 Gene

Regulatory Elements for WHSC1 Gene

Proteins for WHSC1 Gene

  • Protein details for WHSC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O96028-NSD2_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase NSD2
    Protein Accession:
    O96028
    Secondary Accessions:
    • A2A2T2
    • A2A2T3
    • A2A2T4
    • A7MCZ1
    • D3DVQ2
    • O96031
    • Q4VBY8
    • Q672J1
    • Q6IS00
    • Q86V01
    • Q9BZB4
    • Q9UI92
    • Q9UPR2

    Protein attributes for WHSC1 Gene

    Size:
    1365 amino acids
    Molecular mass:
    152258 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA83042.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for WHSC1 Gene

neXtProt entry for WHSC1 Gene

Proteomics data for WHSC1 Gene at MOPED

Selected DME Specific Peptides for WHSC1 Gene

Post-translational modifications for WHSC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains for WHSC1 Gene

Gene Families for WHSC1 Gene

HGNC:
  • PHF :Zinc fingers, PHD-type

UniProtKB/Swiss-Prot:

NSD2_HUMAN
Domain:
  • Contains 1 AWS domain.:
    • O96028
  • Contains 1 HMG box DNA-binding domain.:
    • O96028
  • Contains 1 post-SET domain.:
    • O96028
  • Contains 2 PWWP domains.:
    • O96028
  • Contains 1 SET domain.:
    • O96028
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.:
    • O96028
Similarity:
  • Contains 4 PHD-type zinc fingers.:
    • O96028
genes like me logo Genes that share domains with WHSC1: view

Function for WHSC1 Gene

Molecular function for WHSC1 Gene

GENATLAS Biochemistry: Wolf-Hirschhorn syndrome candidate gene 1,ubiquitously expressed and undergoing complex alternative splicing and differential polyadenylation homolog to Drosophila dysmorphy gene ash,fused to IgH in multiple myeloma with translocation t(4;14)((p16.3;q32) with FGFR3 overexpression
UniProtKB/Swiss-Prot CatalyticActivity: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
UniProtKB/Swiss-Prot Function: Histone methyltransferase with histone H3 Lys-27 (H3K27me) methyltransferase activity. Isoform RE-IIBP may act as a transcription regulator that binds DNA and suppresses IL5 transcription through HDAC recruitment.

Enzyme Numbers (IUBMB) for WHSC1 Gene

Gene Ontology (GO) - Molecular Function for WHSC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 19481544
GO:0008270 zinc ion binding IEA --
GO:0018024 histone-lysine N-methyltransferase activity IEA --
genes like me logo Genes that share ontologies with WHSC1: view
genes like me logo Genes that share phenotypes with WHSC1: view

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for WHSC1 Gene

Localization for WHSC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WHSC1 Gene

Nucleus. Chromosome.
Isoform 4: Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for WHSC1 Gene COMPARTMENTS Subcellular localization image for WHSC1 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for WHSC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005730 nucleolus --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with WHSC1: view

Pathways for WHSC1 Gene

genes like me logo Genes that share pathways with WHSC1: view

Pathways by source for WHSC1 Gene

Gene Ontology (GO) - Biological Process for WHSC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0003149 membranous septum morphogenesis IEA --
GO:0003289 atrial septum primum morphogenesis IEA --
GO:0003290 atrial septum secundum morphogenesis IEA --
GO:0006325 chromatin organization TAS --
genes like me logo Genes that share ontologies with WHSC1: view

Compounds for WHSC1 Gene

(3) HMDB Compounds for WHSC1 Gene

Compound Synonyms Cas Number PubMed IDs
L-Lysine
  • (+)-S-Lysine
56-87-1
S-Adenosylhomocysteine
  • (S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine
979-92-0
S-Adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
29908-03-0
genes like me logo Genes that share compounds with WHSC1: view

Transcripts for WHSC1 Gene

Unigene Clusters for WHSC1 Gene

Wolf-Hirschhorn syndrome candidate 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for WHSC1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13 ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b ·
SP1: - - - - -
SP2: - - - -
SP3: - - - - - -
SP4: - - - - - - -
SP5: - -
SP6:
SP7: - - - -
SP8: - - - -
SP9:
SP10: - - - - - - -
SP11:
SP12:
SP13:
SP14: - - - - - -
SP15: - -
SP16:
SP17: - -
SP18:
SP19:
SP20:
SP21: - - - -
SP22:

ExUns: 16c · 16d ^ 17a · 17b ^ 18a · 18b · 18c · 18d · 18e ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b ^ 26 ^ 27 ^ 28a · 28b ^
SP1: - - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - - - - - -
SP4: - - - - - - - - - - -
SP5: - - - - - - - - - - -
SP6: - - - - -
SP7:
SP8:
SP9: - - - - - - -
SP10:
SP11: - - - - -
SP12: - -
SP13:
SP14: - - - - - - -
SP15:
SP16:
SP17: - - - -
SP18: - - - - - - - -
SP19:
SP20:
SP21:
SP22: -

ExUns: 29a · 29b ^ 30 ^ 31a · 31b · 31c
SP1: -
SP2: -
SP3: -
SP4: -
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:

Relevant External Links for WHSC1 Gene

GeneLoc Exon Structure for
WHSC1
ECgene alternative splicing isoforms for
WHSC1

Expression for WHSC1 Gene

mRNA expression in normal human tissues for WHSC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for WHSC1 Gene

SOURCE GeneReport for Unigene cluster for WHSC1 Gene Hs.113876

mRNA Expression by UniProt/SwissProt for WHSC1 Gene

O96028-NSD2_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expressions with WHSC1: view

Orthologs for WHSC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for WHSC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WHSC1 36
  • 99.71 (n)
  • 99.85 (a)
WHSC1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia WHSC1 36
  • 82.91 (n)
  • 86.45 (a)
WHSC1 37
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia WHSC1 36
  • 88.39 (n)
  • 91.49 (a)
WHSC1 37
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Whsc1 36
  • 87.39 (n)
  • 91.33 (a)
Whsc1 16
Whsc1 37
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia WHSC1 37
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WHSC1 37
  • 79 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Whsc1 36
  • 86.85 (n)
  • 90.82 (a)
chicken
(Gallus gallus)
Aves WHSC1 36
  • 76.93 (n)
  • 81.32 (a)
WHSC1 37
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia WHSC1 37
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia whsc1 36
  • 68.29 (n)
  • 70.42 (a)
zebrafish
(Danio rerio)
Actinopterygii whsc1 36
  • 67.56 (n)
  • 67.72 (a)
whsc1 37
  • 44 (a)
OneToOne
wufc12c04 36
fruit fly
(Drosophila melanogaster)
Insecta Mes-4 37
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-23 37
  • 33 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9549 37
  • 53 (a)
OneToMany
Species with no ortholog for WHSC1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for WHSC1 Gene

ENSEMBL:
Gene Tree for WHSC1 (if available)
TreeFam:
Gene Tree for WHSC1 (if available)

Paralogs for WHSC1 Gene

Selected SIMAP similar genes for WHSC1 Gene using alignment to 8 proteins:

Pseudogenes.org Pseudogenes for WHSC1 Gene

genes like me logo Genes that share paralogs with WHSC1: view

Variants for WHSC1 Gene

Sequence variations from dbSNP and Humsavar for WHSC1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type MAF
rs9679 -- 1,943,285(-) TAAAA(A/C)ACAGC intron-variant, utr-variant-3-prime
rs14647 -- 1,982,108(-) CCCAA(A/C)TGGCA utr-variant-3-prime
rs373763 -- 1,917,779(-) aaaaa(A/G)gaaTA intron-variant
rs410630 -- 1,925,774(-) aaaaa(A/T)atata intron-variant
rs426891 -- 1,931,216(-) AAGGT(A/G)CAGAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for WHSC1 Gene

Variant ID Type Subtype PubMed ID
nsv878328 CNV Loss 21882294
dgv5408n71 CNV Loss 21882294
nsv822437 CNV Loss 20364138
dgv5416n71 CNV Loss 21882294
nsv829836 CNV Loss 17160897
esv27096 CNV Loss 19812545
nsv819354 CNV Gain 19587683
esv2726833 CNV Deletion 23290073
esv2726834 CNV Deletion 23290073
nsv878418 CNV Loss 21882294
nsv878419 CNV Loss 21882294

Relevant External Links for WHSC1 Gene

HapMap Linkage Disequilibrium report
WHSC1
Human Gene Mutation Database (HGMD)
WHSC1

Disorders for WHSC1 Gene

UniProtKB/Swiss-Prot

NSD2_HUMAN
  • Note=A chromosomal aberration involving WHSC1 is a cause of multiple myeloma tumors. Translocation t(4;14)(p16.3;q32.3) with IgH.
  • Note=WHSC1 is located in the Wolf-Hirschhorn syndrome (WHS) critical region. WHS results from by sub-telomeric deletions in the short arm of chromosome 4. WHSC1 is deleted in every case, however deletion of linked genes contributes to both the severity of the core characteristics and the presence of the additional syndromic problems.

(2) University of Copenhagen DISEASES for WHSC1 Gene

(3) Novoseek inferred disease relationships for WHSC1 Gene

Disease -log(P) Hits PubMed IDs
myeloma 66.9 6
tumors 19.2 12
cancer 0 5

Relevant External Links for WHSC1

Genetic Association Database (GAD)
WHSC1
Human Genome Epidemiology (HuGE) Navigator
WHSC1
genes like me logo Genes that share disorders with WHSC1: view

Publications for WHSC1 Gene

  1. WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma. (PMID: 9618163) Stec I. … den Dunnen J.T. (Hum. Mol. Genet. 1998) 2 3 4 23
  2. The t(4;14) translocation in myeloma dysregulates both FGFR3 and a novel gene, MMSET, resulting in IgH/MMSET hybrid transcripts. (PMID: 9787135) Chesi M. … Bergsagel P.L. (Blood 1998) 2 3 4 23
  3. A unique mRNA initiated within a middle intron of WHSC1/MMSET encodes a DNA binding protein that suppresses human IL-5 transcription. (PMID: 11152655) Garlisi C.G. … Umland S.P. (Am. J. Respir. Cell Mol. Biol. 2001) 3 4 23
  4. A subset of multiple myeloma harboring the t(4;14)(p16;q32) translocation lacks FGFR3 expression but maintains an IGH/MMSET fusion transcript. (PMID: 12433679) Santra M. … Shaughnessy J. Jr. (Blood 2003) 3 4 23
  5. Transcription repression activity is associated with the type I isoform of the MMSET gene involved in t(4;14) in multiple myeloma. (PMID: 16197452) Todoerti K. … Neri A. (Br. J. Haematol. 2005) 3 4 23

Products for WHSC1 Gene

Sources for WHSC1 Gene

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